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Crystal structure of human NUDT5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DSD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 30% PEG4000, 0.2M magnesium chloride, 0.1M tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.6 52.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.6 α = 79.92 b = 60.14 β = 81.52 c = 80.01 γ = 75.49
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2018-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.93 43.49 97.5 0.035 7.4 2 64137
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.98
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2DSD 1.93 32.03 60999 3176 97.46 0.23298 0.23115 0.2429 0.2696 0.2811 RANDOM 43.909
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 3.2 1.63 -0.41 -0.61 1.47 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.961 r_dihedral_angle_4_deg 14.935 r_dihedral_angle_3_deg 14.59 r_long_range_B_refined 8.253 r_long_range_B_other 8.253 r_dihedral_angle_1_deg 6.702 r_scangle_other 6.196 r_mcangle_it 5.782 r_mcangle_other 5.782 r_scbond_it 4.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.961 r_dihedral_angle_4_deg 14.935 r_dihedral_angle_3_deg 14.59 r_long_range_B_refined 8.253 r_long_range_B_other 8.253 r_dihedral_angle_1_deg 6.702 r_scangle_other 6.196 r_mcangle_it 5.782 r_mcangle_other 5.782 r_scbond_it 4.36 r_scbond_other 4.359 r_mcbond_it 4.216 r_mcbond_other 4.215 r_angle_refined_deg 1.694 r_angle_other_deg 0.964 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5700 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing